Record Information
Version2.0
Creation Date2012-05-31 13:47:50 -0600
Update Date2015-06-03 15:53:51 -0600
Secondary Accession Numbers
  • ECMDB01213
Identification
Name:1-Deoxy-D-xylulose 5-phosphate
Description:1-Deoxy-D-xylulose 5-phosphate is an intermediate in the non-mevalonate pathway. This is an alternative metabolic pathway leading to the formation of isopentenyl pyrophosphate (IPP) and dimethylallyl pyrophosphate (DMAPP). The key enzyme in the non-mevalonate pathway of isoprenoid biosynthesis is 1-deoxy-D-xylulose 5-phosphate reductoisomerase (DXR).
Structure
Thumb
Synonyms:
  • 1-Deoxy-D-threo-pentulose 5-phosphate
  • 1-Deoxy-D-threo-pentulose 5-phosphoric acid
  • 1-Deoxy-D-xylulose 5-phosphate
  • 1-Deoxy-D-xylulose 5-phosphoric acid
  • 1DX5P
  • D-1-Deoxyxylulose-5-P
  • Deoxyxylulose-5-phosphate
  • Deoxyxylulose-5-phosphoric acid
  • DOXP
  • DXP
Chemical Formula:C5H11O7P
Weight:Average: 214.1104
Monoisotopic: 214.024239218
InChI Key:AJPADPZSRRUGHI-RFZPGFLSSA-N
InChI:InChI=1S/C5H11O7P/c1-3(6)5(8)4(7)2-12-13(9,10)11/h4-5,7-8H,2H2,1H3,(H2,9,10,11)/t4-,5-/m1/s1
CAS number:190079-18-6
IUPAC Name:{[(2R,3S)-2,3-dihydroxy-4-oxopentyl]oxy}phosphonic acid
Traditional IUPAC Name:1-deoxy-D-xylulose-5-phosphate
SMILES:CC(=O)[C@@H](O)[C@H](O)COP(O)(O)=O
Chemical Taxonomy
DescriptionThis compound belongs to the class of chemical entities known as pentose phosphates. These are carbohydrate derivatives containing a pentose substituted by one or more phosphate groups.
KingdomChemical entities
Super ClassOrganic compounds
ClassOrganic oxygen compounds
Sub ClassOrganooxygen compounds
Direct ParentPentose phosphates
Alternative Parents
Substituents
  • Pentose-5-phosphate
  • Monosaccharide phosphate
  • Monoalkyl phosphate
  • Acyloin
  • Beta-hydroxy ketone
  • Alkyl phosphate
  • Phosphoric acid ester
  • Organic phosphoric acid derivative
  • Alpha-hydroxy ketone
  • Ketone
  • 1,2-diol
  • Secondary alcohol
  • Carbonyl group
  • Hydrocarbon derivative
  • Alcohol
  • Organic oxide
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Physical Properties
State:Solid
Charge:-2
Melting point:Not Available
Experimental Properties:
PropertyValueSource
Predicted Properties
PropertyValueSource
Water Solubility27.6 mg/mLALOGPS
logP-1.9ALOGPS
logP-1.9ChemAxon
logS-0.89ALOGPS
pKa (Strongest Acidic)1.48ChemAxon
pKa (Strongest Basic)-3.6ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count6ChemAxon
Hydrogen Donor Count4ChemAxon
Polar Surface Area124.29 Å2ChemAxon
Rotatable Bond Count5ChemAxon
Refractivity40.77 m3·mol-1ChemAxon
Polarizability17.18 Å3ChemAxon
Number of Rings0ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations:Cytoplasm
Reactions:
1-Deoxy-D-xylulose 5-phosphate + NAD + O-Phospho-4-hydroxy-L-threonine > Carbon dioxide + Hydrogen ion +2 Water + NADH + Pyridoxine 5'-phosphate + Phosphate
Adenosine triphosphate + Dehydroglycine + 1-Deoxy-D-xylulose 5-phosphate + Hydrogen ion + IscS with bound sulfur + NADPH > 4-Methyl-5-(2-phosphoethyl)-thiazole + Adenosine monophosphate + Carbon dioxide +2 Water + IscS sulfur acceptor protein + NADP + Pyrophosphate
1-Deoxy-D-xylulose 5-phosphate + Hydrogen ion + NADPH <> 2-C-Methyl-D-erythritol-4-phosphate + NADP
D-Glyceraldehyde 3-phosphate + Hydrogen ion + Pyruvic acid <> Carbon dioxide + 1-Deoxy-D-xylulose 5-phosphate
Adenosine triphosphate + 1-Deoxy-D-xylulose > ADP + 1-Deoxy-D-xylulose 5-phosphate + Hydrogen ion
Pyruvic acid + D-Glyceraldehyde 3-phosphate <> 1-Deoxy-D-xylulose 5-phosphate + Carbon dioxide
2-C-Methyl-D-erythritol-4-phosphate + NADP <> 1-Deoxy-D-xylulose 5-phosphate + NADPH + Hydrogen ion
3-Amino-2-oxopropyl phosphate + 1-Deoxy-D-xylulose 5-phosphate + 3-Amino-2-oxopropyl phosphate <> Pyridoxine 5'-phosphate + Phosphate +2 Water
2-C-Methyl-D-erythritol-4-phosphate + NADP <> Hydrogen ion + 1-Deoxy-D-xylulose 5-phosphate + NADPH
Pyruvic acid + D-Glyceraldehyde 3-phosphate + Hydrogen ion > Carbon dioxide + 1-Deoxy-D-xylulose 5-phosphate
1-Amino-propan-2-one-3-phosphate + 1-Deoxy-D-xylulose 5-phosphate > Hydrogen ion + Pyridoxine 5'-phosphate + Phosphate + Water
Adenosine triphosphate + 1-Deoxy-D-xylulose > Hydrogen ion + 1-Deoxy-D-xylulose 5-phosphate + ADP
2-C-methyl-D-erythritol 4-phosphate + NADP > 1-Deoxy-D-xylulose 5-phosphate + NADPH
Pyruvic acid + D-Glyceraldehyde 3-phosphate > 1-Deoxy-D-xylulose 5-phosphate + Carbon dioxide
1-Deoxy-D-xylulose 5-phosphate + 2-Amino-3-phosphonopropionic acid > Pyridoxine 5'-phosphate + Inorganic phosphate +2 Water
1-Deoxy-D-xylulose 5-phosphate + 2-iminoacetate + thiocarboxy-adenylate-[sulfur-carrier protein ThiS] > 2-((2R,5Z)-2-Carboxy-4-methylthiazol-5(2H)-ylidene)ethyl phosphate + [sulfur-carrier protein ThiS] +2 Water
1-Deoxy-D-xylulose 5-phosphate + 2-iminoacetate <> 2-[(2R,5Z)-2-Carboxy-4-methylthiazol-5(2H)-ylidene]ethyl phosphate +2 Water
1-Deoxy-D-xylulose 5-phosphate + 2-Amino-3-phosphonopropionic acid + 1-Deoxy-D-xylulose 5-phosphate + 2-Amino-3-phosphonopropionic acid > Pyridoxine 5'-phosphate + Phosphate + Hydrogen ion +2 Water
D-Glyceraldehyde 3-phosphate + Pyruvic acid + Hydrogen ion + D-Glyceraldehyde 3-phosphate > 1-Deoxy-D-xylulose 5-phosphate + Carbon dioxide + 1-Deoxy-D-xylulose 5-phosphate
D-Glyceraldehyde 3-phosphate + Hydrogen ion + D-Glyceraldehyde 3-phosphate > Carbon dioxide + 1-Deoxy-D-xylulose 5-phosphate + 1-Deoxy-D-xylulose 5-phosphate
NADPH + Hydrogen ion + 1-Deoxy-D-xylulose 5-phosphate + NADPH + 1-Deoxy-D-xylulose 5-phosphate > NADP + 2-C-methyl-D-erythritol 4-phosphate
D-Glyceraldehyde 3-phosphate + Hydrogen ion + D-Glyceraldehyde 3-phosphate > Carbon dioxide + 1-Deoxy-D-xylulose 5-phosphate + 1-Deoxy-D-xylulose 5-phosphate
1-Deoxy-D-xylulose 5-phosphate + Dehydroglycine + a thiocarboxy-[ThiS-Protein] > 2-((2R,5Z)-2-Carboxy-4-methylthiazol-5(2H)-ylidene)ethyl phosphate + a ThiS sulfur-carrier protein +2 Water
D-Glyceraldehyde 3-phosphate + Pyruvic acid + Hydrogen ion > 1-Deoxy-D-xylulose 5-phosphate + Carbon dioxide
SMPDB Pathways:
Secondary metabolites: isoprenoid biosynthesis (nonmevalonate pathway)PW000975 Pw000975Pw000975 greyscalePw000975 simple
Secondary metabolites: methylerythritol phosphate and polyisoprenoid biosynthesisPW000958 Pw000958Pw000958 greyscalePw000958 simple
Thiazole Biosynthesis IPW002041 Pw002041Pw002041 greyscalePw002041 simple
Vitamin B6 1430936196PW000891 Pw000891Pw000891 greyscalePw000891 simple
KEGG Pathways:
EcoCyc Pathways:
Concentrations
Not Available
Spectra
Spectra:
Spectrum TypeDescriptionSplash Key
GC-MSGC-MS Spectrum - GC-MSsplash10-0007-9500000000-8bdb536a3dd0ef5e39ffView in MoNA
GC-MSGC-MS Spectrum - GC-MS (2 TMS)splash10-03dj-7591000000-ee5996fd8cd465a4edc0View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-014j-2940000000-5e70f58c1f6619c74596View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0005-7900000000-67299c05b993067eaee5View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0005-9200000000-303ff032b1dd45390bacView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-00di-9320000000-41ec442dafa3cc090e2dView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-004i-9100000000-5d0fcbc94e864a9d2006View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-004i-9000000000-2ee0f7b4883b35fcb552View in MoNA
References
References:
  • Kanehisa, M., Goto, S., Sato, Y., Furumichi, M., Tanabe, M. (2012). "KEGG for integration and interpretation of large-scale molecular data sets." Nucleic Acids Res 40:D109-D114. Pubmed: 22080510
  • Keseler, I. M., Collado-Vides, J., Santos-Zavaleta, A., Peralta-Gil, M., Gama-Castro, S., Muniz-Rascado, L., Bonavides-Martinez, C., Paley, S., Krummenacker, M., Altman, T., Kaipa, P., Spaulding, A., Pacheco, J., Latendresse, M., Fulcher, C., Sarker, M., Shearer, A. G., Mackie, A., Paulsen, I., Gunsalus, R. P., Karp, P. D. (2011). "EcoCyc: a comprehensive database of Escherichia coli biology." Nucleic Acids Res 39:D583-D590. Pubmed: 21097882
  • van der Werf, M. J., Overkamp, K. M., Muilwijk, B., Coulier, L., Hankemeier, T. (2007). "Microbial metabolomics: toward a platform with full metabolome coverage." Anal Biochem 370:17-25. Pubmed: 17765195
Synthesis Reference:Blagg, Brian S. J.; Poulter, C. Dale. Synthesis of 1-Deoxy-D-xylulose and 1-Deoxy-D-xylulose-5-phosphate. Journal of Organic Chemistry (1999), 64(5), 1508-1511.
Material Safety Data Sheet (MSDS)Not Available
External Links:
ResourceLink
CHEBI ID16493
HMDB IDHMDB01213
Pubchem Compound ID443201
Kegg IDC11437
ChemSpider ID391473
Wikipedia1-Deoxy-D-xylulose 5-phosphate
BioCyc IDDEOXYXYLULOSE-5P
EcoCyc IDDEOXYXYLULOSE-5P
Ligand ExpoDXP

Enzymes

General function:
Involved in phosphotransferase activity, alcohol group as acceptor
Specific function:
ATP + D-xylulose = ADP + D-xylulose 5- phosphate
Gene Name:
xylB
Uniprot ID:
P09099
Molecular weight:
52618
Reactions
ATP + D-xylulose = ADP + D-xylulose 5-phosphate.
General function:
Involved in metabolic process
Specific function:
Catalyzes the removal of elemental sulfur and selenium atoms from cysteine and selenocysteine to produce alanine. Functions as a sulfur delivery protein for NAD, biotin and Fe-S cluster synthesis. Transfers sulfur on 'Cys-456' of thiI in a transpersulfidation reaction. Transfers sulfur on 'Cys-19' of tusA in a transpersulfidation reaction. Functions also as a selenium delivery protein in the pathway for the biosynthesis of selenophosphate
Gene Name:
iscS
Uniprot ID:
P0A6B7
Molecular weight:
45089
Reactions
L-cysteine + acceptor = L-alanine + S-sulfanyl-acceptor.
General function:
Involved in catalytic activity
Specific function:
Catalyzes the complicated ring closure reaction between the two acyclic compounds 1-deoxy-D-xylulose-5-phosphate (DXP) and 3-amino-2-oxopropyl phosphate (1-amino-acetone-3-phosphate or AAP) to form pyridoxine 5'-phosphate (PNP) and inorganic phosphate
Gene Name:
pdxJ
Uniprot ID:
P0A794
Molecular weight:
26384
Reactions
1-deoxy-D-xylulose 5-phosphate + 3-amino-2-oxopropyl phosphate = pyridoxine 5'-phosphate + phosphate + 2 H(2)O.
General function:
Involved in 4-hydroxythreonine-4-phosphate dehydrogenase activity
Specific function:
Catalyzes the NAD(P)-dependent oxidation of 4- (phosphohydroxy)-L-threonine (HTP) into 2-amino-3-oxo-4- (phosphohydroxy)butyric acid which spontaneously decarboxylates to form 3-amino-2-oxopropyl phosphate (AHAP)
Gene Name:
pdxA
Uniprot ID:
P19624
Molecular weight:
35114
Reactions
4-(phosphonooxy)-L-threonine + NAD(+) = (2S)-2-amino-3-oxo-4-phosphonooxybutanoate + NADH.
General function:
Involved in 1-deoxy-D-xylulose-5-phosphate reductoisomerase activity
Specific function:
Catalyzes the NADP-dependent rearrangement and reduction of 1-deoxy-D-xylulose-5-phosphate (DXP) to 2-C-methyl-D-erythritol 4-phosphate (MEP)
Gene Name:
dxr
Uniprot ID:
P45568
Molecular weight:
43388
Reactions
2-C-methyl-D-erythritol 4-phosphate + NADP(+) = 1-deoxy-D-xylulose 5-phosphate + NADPH.
General function:
Involved in 1-deoxy-D-xylulose-5-phosphate synthase activity
Specific function:
Catalyzes the acyloin condensation reaction between C atoms 2 and 3 of pyruvate and glyceraldehyde 3-phosphate to yield 1-deoxy-D-xylulose-5-phosphate (DXP)
Gene Name:
dxs
Uniprot ID:
P77488
Molecular weight:
67616
Reactions
Pyruvate + D-glyceraldehyde 3-phosphate = 1-deoxy-D-xylulose 5-phosphate + CO(2).
General function:
Involved in nucleotide binding
Specific function:
Catalyzes the adenylation by ATP of the carboxyl group of the C-terminal glycine of sulfur carrier protein ThiS
Gene Name:
thiF
Uniprot ID:
P30138
Molecular weight:
26970
Reactions
ATP + [ThiS] = diphosphate + adenylyl-[ThiS].
General function:
Involved in RNA binding
Specific function:
Catalyzes the ATP-dependent transfer of a sulfur to tRNA to produce 4-thiouridine in position 8 of tRNAs, which functions as a near-UV photosensor. Also catalyzes the transfer of sulfur to the sulfur carrier protein ThiS, forming ThiS-thiocarboxylate. This is a step in the synthesis of thiazole, in the thiamine biosynthesis pathway. The sulfur is donated as persulfide by iscS
Gene Name:
thiI
Uniprot ID:
P77718
Molecular weight:
54973
Reactions
L-cysteine + 'activated' tRNA = L-serine + tRNA containing a thionucleotide.
[IscS]-SSH + [ThiS]-COAMP = [IscS]-SH + [ThiS]-COSH + AMP.
General function:
Involved in catalytic activity
Specific function:
Catalyzes the rearrangement of 1-deoxy-D-xylulose 5- phosphate (DXP) to produce the thiazole phosphate moiety of thiamine. Sulfur is provided by the thiocarboxylate moiety of the carrier protein ThiS. In vitro, sulfur can be provided by H(2)S
Gene Name:
thiG
Uniprot ID:
P30139
Molecular weight:
26896
Reactions
1-deoxy-D-xylulose 5-phosphate + 2-iminoacetate + thiocarboxy-adenylate-[sulfur-carrier protein ThiS] = 2-((2R,5Z)-2-carboxy-4-methylthiazol-5(2H)-ylidene)ethyl phosphate + [sulfur-carrier protein ThiS] + 2 H(2)O.
General function:
Coenzyme transport and metabolism
Specific function:
Is the sulfur donor in the synthesis of the thiazole phosphate moiety of thiamine phosphate
Gene Name:
thiS
Uniprot ID:
O32583
Molecular weight:
7311
General function:
Involved in catalytic activity
Specific function:
Catalyzes the radical-mediated cleavage of tyrosine to dehydroglycine and p-cresol
Gene Name:
thiH
Uniprot ID:
P30140
Molecular weight:
43320
Reactions
L-tyrosine + S-adenosyl-L-methionine + reduced acceptor = 2-iminoacetate + 4-methylphenol + 5'-deoxyadenosine + L-methionine + acceptor + 2 H(+).